Using first-principles calculations, we show that the magnetic properties of a two-dimensional antiferromagnetic transition-metal surface are modified on the atomic scale by the adsorption of small organic molecules. We consider benzene (C6H6), cyclooctatetraene (C8H8) and a small transition metal - benzene complex (BzV) adsorbed on a single atomic layer of Mn deposited on the W(110) surface -- a surface which exhibits a nearly antiferromagnetic alignment of the magnetic moments in adjacent Mn rows. Due to the spin-dependent hybridization of the molecular pz orbitals with the d states of the Mn monolayer there is a significant reduction of the magnetic moments in the Mn film. Furthermore, the spin-polarization at this organic-antiferromagnetic interface is found to be modulated on the atomic scale, both enhanced and inverted, as a result of the molecular adsorption. We show that this effect can be resolved by spin-polarized scanning tunneling microscopy (SP-STM). Our simulated SP-STM images display a spatially-dependent spin-resolved vacuum charge density above an adsorbed molecule -- i.e., different regions above the molecule sustain different signs of spin polarization. While states with s and p symmetry dominate the vacuum charge density in the vicinity of the Fermi energy for the clean magnetic surface, we demonstrate that after a molecule is adsorbed those d-states, which are normally suppressed due to their symmetry, can play a crucial role in the vacuum due to their interaction with the molecular orbitals. We also model the effect of small deviations from perfect antiferromagnetic ordering, induced by the slight canting of magnetic moments due to the spin spiral ground state of Mn/W(110).